OBJECTIVES: To analyse the effect of a 24-week physical training programme in water and on land on women with fibromyalgia. METHODS: A controlled study was conducted from December 2009 to May 2010. Seventy-two women with fibromyalgia (age: 51.79±7.87 years) were assigned to an exercise group (3 sessions/week, 2 sessions in water, 1 session on land) (n=42) and to a control group (n=30). The variables analysed were: number of tender points, visual analogue scale (VAS) of pain, algometer score, functional capacity (leg strength, hand-grip dynamometry, flexibility, agility, balance, aerobic endurance, heart response), body composition (body mass index, fat mass index, skeletal muscle mass index and percentage of body fat) and psychological variables (Fibromyalgia Impact Questionnaire [FIQ] and Short Form Health Survey 36 [SF-36]). RESULTS: The exercise group improved in the algometer score (p<0.001), positive tender points (p=0.005), VAS (p<0.001) and FIQ (p<0.001). Improvements were also detected in functional capacity (leg strength, p=0.001; hand-grip dynamometry, p=0.001; flexibility, p<0.001; balance, p=0.006; 6-minute walk test, p<0.001; mean heart rate, p=0.031; maximum heart rate, p<0.001 and VO2 max, p<0.001). There was a decrease in the percentage of body fat (p=0.040). There was also an improvement in the subscales of the SF-36; vitality (p=0.004), mental health (p=0.001) social role functioning (p=0.020) and general health functioning (p=0.002). CONCLUSIONS: The findings of this study show that a 24-week physical training programme (3 sessions/week, of which 2 sessions are in water and 1 session is on land) reduces pain and disease impact and improves functional capacity in women with fibromyalgia.